Major Clusters Research Articles

Quality of life and socio-demographic factors associated with nutritional risk in Brazilian community-dwelling individuals aged 80 and over: cluster analysis and ensemble methods.

The aim of the present study was to use cluster analysis and ensemble methods to evaluate the association between quality of life, socio-demographic factors to predict nutritional risk in community-dwelling Brazilians aged 80 and over. This cross-sectional study included 104 individuals, both sexes, from different community locations. Firstly, the participants answered the sociodemographic questionnaire, and were sampled for anthropometric data. Subsequently, the Mini-Mental State Examination (MMSE) was applied, and Mini Nutritional Assessment Questionnaire (MAN) was used to evaluate their nutritional status. Finally, quality of life (QoL) was assessed by a brief version of World Health Organizations' Quality of Life (WHOQOL-BREF) questionnaire and its older adults' version (WHOQOL-OLD). The K-means algorithm was used to identify clusters of individuals regarding quality-of-life characteristics. In addition, Random Forest (RF) and eXtreme Gradient Boosting (XGBoost) algorithms were used to predict nutritional risk. Four major clusters were derived. Although there was a higher proportion of individuals aged 80 and over with nutritional risk in cluster 2 and a lower proportion in cluster 3, there was no statistically significant association. Cluster 1 showed the highest scores for psychological, social, and environmental domains, while cluster 4 exhibited the worst scores for the social and environmental domains of WHOQOL-BREF and for autonomy, past, present, and future activities, and intimacy of WHOQOL-OLD. Handgrip, household income, and MMSE were the most important predictors of nutritional. On the other hand, sex, self-reported health, and number of teeth showed the lowest levels of influence in the construction of models to evaluate nutritional risk. Taken together, there was no association between clusters based on quality-of-life domains and nutritional risk, however, predictive models can be used as a complementary tool to evaluate nutritional risk in individuals aged 80 and over.

Genetic variations among the isolates of Bipolaris Maydis based on phenotypic and molecular markers

Abstract Maydis leaf blight, caused by Bipolaris maydis, is an important disease of maize crop in Khyber Pakhtunkhwa (KP) Pakistan. Fifteen isolates of the pathogen, collected across KP, were studied for variability based on phenotypic and molecular markers. Significant variability among the isolates was observed when assessed using phenotypic traits such as radial growth, spore concentration, fungicide sensitivity and virulence. The isolates were classified into six culture groups based on colour, texture and margins of the colony. Conidial morphology was also variable. These were either straight or slightly curved and light to dark brown in colour. Fungicide test showed significant variation in the degree of sensitivity against Carbendazim. Isolate Bm8 exhibited maximum radial growth on carbendazim spiked plates. Conversely, isolate Bm15 showed the lowest radial growth. Variations in virulence pattern of the isolates were evident when a susceptible maize variety Azam was inoculated with spores of B. maydis. Genetic variability amongst the isolates was also estimated by RAPD as well as sequencing of ITS region. The RAPD dendrogram grouped all the isolates into two major clusters. Average genetic distance ranged from 0.6% to 100%, indicating a diverse genetic gap among the isolates. Maximum genetic distance was found between isolates Bm9 and Bm10 as well as Bm2 and Bm8. Conversely, isolates Bm13 and Bm15 were at minimum genetic distance. Phylogenetic dendrogram based on sequencing of ITS region grouped all the isolates into a single major cluster. The clusters in both the dendrogram neither correlate to the geographical distribution nor to the morphological characteristics.

Genetic population structure of the Vietnamese ginseng (Panax vietnamensis Ha et Grushv.) detected by microsatellite analysis.

Panax vietnamensis Ha et Grushv. is a precious medicinal species native to the tropical forests of Vietnam. Due to habitat loss and over-harvesting, this species is endangered in Vietnam. To conserve the species, we investigated genetic variability and population structure using nine microsatellites for 148 individuals from seven populations across the current distribution range of P. vietnamensis in Vietnam. We determined a moderate genetic diversity within populations (HO = 0.367, HE = 0.437) and relatively low population differentiation (the Weir and Cockerham index of 0.172 and the Hedrick index of 0.254) and showed significant differentiation (P < 0.05), which suggested fragmented habitats, over-utilization and over-harvesting of P. vietnamensis. Different clustering methods revealed that individuals were grouped into two major clusters, which were associated with gene flow across the geographical range of P. vietnamensis. This study also detected that ginseng populations can have undergone a recent bottleneck. We recommend measures in future P. vietnamensis conservation and breeding programs.

Molecular characterization of oats (Avena sativa L.) diversity: Implications for dual-purpose breeding

Oat (Avena sativa L.) is one of the world's healthiest and gluten-free grains that are packed with essential vitamins, minerals, fiber, and antioxidants. It is also one of the most important cereal fodder crops. The present study was conducted from 2016 to 2018 and morphological and molecular diversity was analyzed for dual-purpose oat based on ten fodder and eight grain traits among 96 oats accessions including four wild accessions (A. vavilioviana, Guiena oats, A. maroccana and A. sterilis) collected from various eco-geographical regions of India. Thirty-one out of one hundred seventy (18%) simple sequence repeats (SSR) markers detected polymorphism among the 96 oat accessions with average polymorphic information content (PIC) of 0.47. A total of 100 alleles were detected with an average of 3.2 alleles per primer. The molecular diversity analysis grouped all the 96 germplasm lines into two major clusters, ?A? and ?B?. The similarity coefficients ranged from 0.37 to 1. The genotypic pairs viz; UPO 276: SKO 315 (46%); SKO 314: OL-125 (46%); SKO 314: OS 363 (49%); SKO 314: UPO 032 (49%) exhibited least genetic similarity and these pairs can be potentially used as parents to conduct various mapping studies and further contributing to the oat breeding community. Moreover, 6 accessions (JHO-2001-1, JHO-99-2, OL 1635, SKO 27, UPO 093 and OS329) had been identified which were superior to OL-10 (best check in the northwest India) for fodder as well as grain yield. This study showed the opportunity of utilizing SSR markers with morphological characteristics to breed for dual purpose oats.

Early-stage volume losses in the corpus callosum and thalamus predict the progression of brain atrophy in patients with multiple sclerosis

BackgroundA method that can be used in the early stage of multiple sclerosis (MS) to predict the progression of brain volume loss (BVL) has not been fully established. MethodsTo develop a method of predicting progressive BVL in patients with MS (pwMS), eighty-two consecutive Japanese pwMS—with either relapsing-remitting MS (86%) or secondary progressive MS (14%)—and 41 healthy controls were included in this longitudinal retrospective analysis over an observational period of approximately 3.5 years. Using a hierarchical cluster analysis with multivariate imaging data obtained by FreeSurfer analysis, we classified the pwMS into clusters. ResultsAt baseline and follow-up, pwMS were cross-sectionally classified into three major clusters (Clusters 1, 2, and 3) in ascending order by disability and BVL. Among the patients included in Cluster 1 at baseline, approximately one-third of patients (12/52) transitioned into Cluster 2 at follow-up. The volumes of the corpus callosum, the thalamus, and the whole brain excluding the ventricles were significantly decreased in the transition group compared with the nontransition group and were found to be the most important predictors of transition. ConclusionDecreased volumes of the corpus callosum and thalamus in the relatively early stage of MS may predict the development of BVL.

Crowdfunding as a Social Phenomenon: A Bibliometric Exploration of Research Trends and Societal Implications

From a marginal to a relevant social phenomenon, crowdfunding has changed traditional funding patterns and caused far-reaching consequences in most areas of society. Actually, very little is known about the multi-faceted implications brought about by crowdfunding. Grounded on existing research, this paper contributes to an understanding of the overall societal impact created by crowdfunding through a bibliometric analysis. This methodology applies co-citation analysis, citation analysis, and keyword co-occurrence analysis to 561 journal publications retrieved from Scopus until August 2024. The results show that there are five major research clusters: Financial Technology and Consumer Behaviour, Entrepreneurial Finance and Innovation, Economic Impact and Business Models, Islamic Finance and Crowdfunding, and Social Impact and Public Goods. The paper contextualises crowdfunding within the framework of democratising access to capital, innovation, and social causes. It also underlines the integration of Islamic finance principles into crowdfunding models. The research set’s theoretical implications serve as the foundation for revised frameworks on entrepreneurship, venture capital, and social impact assessment, which incorporate the influence of crowdfunding. Platform operators, project creators, and investors need to adapt their strategies to evolving consumer behaviours, comprehend backer motivations, and take into account the wider societal impact of the projects they fund. The present research enables future studies of crowdfunding in terms of long-term impact and is a valuable insight for scholars, practitioners, and policymakers to steer their way forward in this fast-changing field.

Morphological and molecular diversity of eggplant accessions (Solanum melongena L) using Simple Sequence Repeats (SSR) markers

The evaluation of various desirable characteristics in eggplant genotypes has facilitated the efficient process of selecting and improving their traits. Morphological parameters have proven to be valuable in assessing the similarities or differences among different accessions, while molecular data have been used to support the conclusions drawn from the morphological analysis. This study was conducted to evaluate the performance of 42 eggplant genotypes collected from Malaysia, China, and Thailand. Data for growth, yield, and related traits were collected and subjected to analysis of variance (ANOVA) using SAS 9.4. The field trial experiment was designed as a completely randomized block design with three replications. Analysis of variance (ANOVA) showed that the traits under study were highly significant (p &amp;le; 0.01). MV18 (5.97 kg) and TV17 (5.59 kg) were observed to have high yields per plant. The SSR markers used exhibited moderate average values for the number of alleles (2.53). The major allele frequency displayed a high average value (0.53) and a moderate average number of effective alleles (2.31). Additionally, the observed Shannon&amp;apos;s information index, expected heterozygosity, and PIC were high (0.84, 0.54, and 0.45, respectively). 42 accessions were grouped into five major clusters based on similarities using the unweighted pair-group method with arithmetic averages based on similarity matrices UPGMA Dendrogram and the EIGEN module. The findings of this study indicate that the use of simple sequence repeat (SSR) markers can effectively estimate genetic diversity and analyze phylogenetic relationships. Moreover, these markers can assist eggplant breeders in selecting desirable quantitative traits within their breeding program.

Exploring virtual and augmented reality in the hospitality industry: A bibliometric analysis

Purpose – Virtual reality (VR) and augmented reality (AR) technologies are evolving, with scholars highlighting important roles and potential advantages for their use, particularly in the hospitality sector. This bibliometric study examined VR/AR research in the hospitality industry to take stock of the literature in this field and consider potential future directions. Methodology/Design/Approach – Using the Web of Science database, 213 relevant articles were selected and analyzed. Descriptive analysis was conducted using RStudio to identify the most productive countries, journals, authors, and institutions. The most influential topics were identified using keyword co-occurrence analysis in VOSviewer. Findings – The results revealed that VR/AR research in the hospitality sector has recently gained prominence, with China leading in contributions. Three major clusters of themes emerged: (i) the impact of VR on hospitality, tourism, and destinations; (ii) technology enhancing satisfaction and performance in hotels ; and (iii) user acceptance of AR in travel. Originality of the research – This study offers an overview of VR/AR research trends in the hospitality industry based on a bibliometric analysis of literature data from the Web of Science database. It provides research mapping to identify current developments in the VR/ AR literature within this industry and sheds light on areas for future research.

The determinants of COVID-19 case reporting across Africa.

According to study on the under-estimation of COVID-19 cases in African countries, the average daily case reporting rate was only 5.37% in the initial phase of the outbreak when there was little or no control measures. In this work, we aimed to identify the determinants of the case reporting and classify the African countries using the case reporting rates and the significant determinants. We used the COVID-19 daily case reporting rate estimated in the previous paper for 54 African countries as the response variable and 34 variables from demographics, socioeconomic, religion, education, and public health categories as the predictors. We adopted a generalized additive model with cubic spline for continuous predictors and linear relationship for categorical predictors to identify the significant covariates. In addition, we performed Hierarchical Clustering on Principal Components (HCPC) analysis on the reporting rates and significant continuous covariates of all countries. 21 covariates were identified as significantly associated with COVID-19 case detection: total population, urban population, median age, life expectancy, GDP, democracy index, corruption, voice accountability, social media, internet filtering, air transport, human development index, literacy, Islam population, number of physicians, number of nurses, global health security, malaria incidence, diabetes incidence, lower respiratory and cardiovascular diseases prevalence. HCPC resulted in three major clusters for the 54 African countries: northern, southern and central essentially, with the northern having the best early case detection, followed by the southern and the central. Overall, northern and southern Africa had better early COVID-19 case identification compared to the central. There are a number of demographics, socioeconomic, public health factors that exhibited significant association with the early case detection.

Specific cell subclusters of dental pulp stem cells respond to distinct pathogens through the ROS pathway.

Microbial pathogens invade various human organs, including the oral cavity. Candida albicans (C.a) and Streptococcus mutans (S.m) served respectively as representative oral pathogenic fungi and bacteria to stimulate dental pulp stem cells (DPSCs) and to screen the DPSC subcluster that specifically responded to fungal infection. DPSCs were obtained from the impacted third molars of six healthy subjects. Then, cells were mixed and divided into three samples, two of which were stimulated with C.a and S.m, respectively; the third sample was exposed to cell medium only (Ctrl). Single-cell mRNA sequencing analysis of treated DPSCs was performed. DPSCs were composed of four major clusters of which one, DPSC.7, exhibited unique changes compared to those of other subclusters. The DPSC.7 cell percentage of the C.a sample was twice those of the Ctrl and S.m samples. DPSC.7 cells expressed genes associated with the response to reactive oxygen species (ROS) response. DPSC.7 subgroup cells established characteristic aggregation under the stimulation of different pathogens in UMAP. The MAPK/ERK1/2 and NF-κB pathways were up-regulated, DUSP1/5/6 expressions were suppressed, FOS synthesis was activated, the immune-related pathway was induced, and the levels of cytokines, including IL-6 and CCL2, were up-regulated in DPSC.7 cells when stimulated with C.a. Our study analyzed the cellular and molecular properties of DPSCs infected by oral fungi and bacteria with single-cell RNA sequencing. A subcluster of DPSCs responded specifically to infections with different pathogens, activating the MAPK and NF-κB pathways to induce immune responses via the ROS pathway. This suggests novel treatment strategies for fungal infections.

제2외국어 교육에서의 리터러시에 관한 국제 연구 동향 분석

Objectives This study conducted keyword network analysis to understand recent research trends in the field of second language education. Through this, the study aimed to comprehend the changes in research topics and directions and suggest future orientations in the field.&#x0D; Methods For this research, a keyword network analysis was conducted based on keywords extracted from various academic journals and papers. During the period from May to July 2023, topics and abstracts of papers were gathered from various academic databases, and keywords were organized accordingly. These organized keywords underwent a process of frequency extraction, cleansing, network matrix creation, centrality analysis, and visualization. Through this method, the study evaluated the relationship between major research topics, assessing centrality, clustering, and connectivity.&#x0D; Results The analysis revealed distinct keyword and research topic differences between the fields of ESL (English as a Second Language) and ELF (English as a Lingua Franca). In the ESL field, topics such as ‘language acquisition,’ ‘textbook evaluation,’ and ‘teacher training’ were prominently addressed. However, in the ELF field, research emphasized ‘recognition of diversity,’ ‘educational strategies,’ and ‘cultural flexibility.’ Additionally, studies on literacy elements emphasized the importance of modern second language education, with active discussions on the methods and effects of integrating technology into teaching.&#x0D; Conclusions Through keyword network analysis, research trends and key subjects in the field of second language education were identified. These findings provide significant insights for future research directions and offer valuable perspectives for educators and researchers.&#x0D;

Bibliometric analysis and research directions concerning visualization of workplace spirituality

Workplace spirituality has become a significant area for research in recent years due to its ability to benefit employees and improve organizational performance. This research paper analyzes the development of workplace spirituality from 2003 to 2022, with an emphasis on its potential outcomes. Using VOS viewer software, a bibliometric study is performed on a sample of 478 articles from the Scopus database. The study presents various bibliometric indicators, including the number of publications, subject areas, most influential authors, journals, and countries; citation and cocitation maps of authors and journals; and the identification of nineteen central themes and three clusters through co-occurrence analysis. The study also highlights the three major clusters: workplace spirituality and organizational performance, workplace spirituality and leadership, and spirituality and well-being. The paper discusses the various theories and methods used in the WPS literature and provides insights into future research directions. The findings of this study have important implications for scholars and practitioners interested in enhancing the performance of employees and organizations.

Assessment of Genetic Diversity among the Elite Rose (Rosa spp.) Accessions Using Rapd Markers

Aims: Owing to its export value in flower trade elsewhere in the world, Rose is the key commercial flower crop and the area under rose cultivation is ever increasing and the end-users always prefer new color variations. Hence, evolving new cultivars with novel color characteristics is the need of the hour, for which understanding genetic variation in the available cultivars is very much needed. &#x0D; Study Design: This investigation was conducted to analyze the genetic diversity of 11 elite and commonly cultivated rose accessions in South India by using randomly amplified polymorphic DNA (RAPD) markers.&#x0D; Place and Duration of Study: Department of Floriculture and Landscape Architecture, Horticultural College and Research Institute, TNAU, Coimbatore.&#x0D; Methodology: A total of 10 RAPD primers were employed, which was sufficient to distinguish the investigated rose cultivars.&#x0D; Results: Among the 44 PCR products produced by these markers, 39 (88.64%) were found to be polymorphic bands. The number of amplified products per RAPD primer varied from 3 to 8 with a mean of 4.4 bands per primer. The Un weighted paired group of arithmetic means (UPGMA) dendrogram distinguished the rose accessions into two major clusters suggesting that the accessions were different from each other. The genetic similarity coefficients were determined with this RAPD data, and they were ranged from 0.59 to 0.89.&#x0D; Conclusion: Molecular profiling data of this study have contributed to characterize and catalogue the rose germplasm data, which will be useful to identify the diverse rose lines for further breeding program that have the potential to improve the color variations.

EXPLORING THE DYNAMICS OF DEFENSE EXPENDITURE AND ECONOMIC DEVELOPMENT: A BIBLIOMETRIC ANALYSIS

This study used bibliometric analysis to derive meaningful insights from the literature related to the field of defense expenditure and economic development. The analysis covered 381 documents published across a range of journals from 1991–2021. The Scopus database and the bibliometric R package (R studio) were utilized to identify prominent journals, authors, countries, articles, and themes in the area under study. The study's findings revealed a noticeable increase in publications and citations over the years, indicating a positive yearly growth rate of 2.16%. Among the 161 journals examined, Defence and Peace Economics was found to be the most impactful, with 99 published articles, 1,743 citations, an h-index of 25, and a g-index of 34. Moreover, Dunne JP published the most papers, consistently remained the most cited author, and continued to be the most influential author, with an h-index of 12. The USA, China, and Greece produced the highest number of articles, while the collaborative networks of countries were divided into four major clusters, with researchers from the USA collaborating the most with researchers from other countries and the University of Cape Town and COMSATS Institute of Information Technology collaborating the most with other universities.

Karyotypes and Physical Mapping of Ribosomal DNA with Oligo-Probes in Eranthis sect. Eranthis (Ranunculaceae).

A comparative karyotype analysis of four species of yellow-flowered Eranthis sect. Eranthis, i.e., E. bulgarica, E. cilicica, E. hyemalis, and E. longistipitata from different areas, has been carried out for the first time. All the studied specimens had somatic chromosome number 2n = 16 with basic chromosome number x = 8. Karyotypes of the investigated plants included five pairs of metacentric chromosomes and three pairs of submetacentric/subtelocentric chromosomes. The chromosome sets of the investigated species differ mainly in the ratio of submetacentric/subtelocentric chromosomes, their relative lengths, and arm ratios. A new oligonucleotide probe was developed and tested to detect 45S rDNA clusters. Using this probe and an oligonucleotide probe to 5S rDNA, 45S and 5S rDNA clusters were localized for the first time on chromosomes of E. cilicica, E. hyemalis, and E. longistipitata. Major 45S rDNA clusters were identified on satellite chromosomes in all the species; in E. cilicica, minor clusters were also identified in the terminal regions of one metacentric chromosome pair. The number and distribution of 5S rDNA clusters is more specific. In E. cilicica, two major clusters were identified in the pericentromeric region of a pair of metacentric chromosomes. Two major clusters in the pericentromeric region of a pair of submetacentric chromosomes and two major clusters in the interstitial region of a pair of metacentric chromosomes were observed in E. longistipitata. E. hyemalis has many clusters of different sizes, localized mainly in the pericentromeric regions. Summarizing new data on the karyotype structure of E. sect. Eranthis and previously obtained data on E. sect. Shibateranthis allowed conclusions to be formed about the clear interspecific karyological differences of the genus Eranthis.

Genome-Wide in Silico Analysis of the Heat Shock Protein (HSP) Family in Vigna Species: Insights into Molecular Mechanisms of Stress Response

Heat shock proteins, HSPs, are essential for plants to develop defense systems against various abiotic challenges. Vigna species are widely grown cash crops in the world. However, some unfavorable environmental conditions hinder the growth and production of these crops. It is therefore essential to investigate the factors influencing their growth, development, and tolerance to abiotic stress to develop stress-tolerant varieties. Consequently, a comprehensive genome-wide identification study was conducted to identify the Heat Shock Factor (HSF) genes in three Vigna species genomes employing computational tools. In the current study, 43 non-redundant HSP proteins were identified in three Vigna species including 17 in Vigna angularis, 22 in Vigna radiata, and 4 non-redundant in V. ungucuilata. Moreover, subcellular locations were predicted, and all HSPs were found in the nucleus. The theoretical isoelectric point predicted that most of the HSP proteins were acidic. The aliphatic index of the HSP proteins demonstrated that all proteins are highly thermostable. Moreover, the instability index revealed two proteins VangHSP_9 and VradHSP_9, considered stable while the rest of the HSP proteins were unstable. The phylogenetic analysis categorized HSP genes into two major clusters and gene structure analysis displayed that all HSP genes were intronless. This study gives novel insight into the functional characterization of HSPs in Vigna species for plant breeding programs.

Hotspot Regions of Quantitative Trait Loci and Candidate Genes for Ear-Related Traits in Maize: A Literature Review.

In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past three decades. This review aims to (1) comprehensively summarize and analyze previous studies on QTLs associated with these eight ear-related traits and identify hotspot bin regions located on maize chromosomes and key candidate genes associated with the ear-related traits and (2) compile major and stable QTLs and QTL clusters from various mapping populations and mapping methods and techniques providing valuable insights for fine mapping, gene cloning, and breeding for high-yield and high-quality maize. Previous research has demonstrated that QTLs for ear-related traits are distributed across all ten chromosomes in maize, and the phenotypic variation explained by a single QTL ranged from 0.40% to 36.76%. In total, 23 QTL hotspot bins for ear-related traits were identified across all ten chromosomes. The most prominent hotspot region is bin 4.08 on chromosome 4 with 15 QTLs related to eight ear-related traits. Additionally, this study identified 48 candidate genes associated with ear-related traits. Out of these, five have been cloned and validated, while twenty-eight candidate genes located in the QTL hotspots were defined by this study. This review offers a deeper understanding of the advancements in QTL mapping and the identification of key candidates associated with eight ear-related traits. These insights will undoubtedly assist maize breeders in formulating strategies to develop higher-yield maize varieties, contributing to global food security.

Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin

Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistance genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network (SSN) analysis classified 353 Cph homologues into five major clusters, where the proteins in cluster I were found in a broad range of actinobacteria. We examine the function and antibiotics targeted by three putative resistance proteins in cluster I via biochemical and protein structural analysis. Our findings reveal that these three proteins in cluster I confer resistance to CMN, highlighting an important aspect of CMN resistance within this gene family. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.

The population structure of vancomycin-resistant and -susceptible Enterococcus faecium in a low-prevalence antimicrobial resistance setting is highly influenced by circulating global hospital-associated clones.

Between 2010 and 2015 the incidence of vancomycin-resistant Enterococcus faecium (VREfm) in Norway increased dramatically. Hence, we selected (1) a random subset of vancomycin-resistant enterococci (VRE) from the Norwegian Surveillance System for Communicable Diseases (2010-15; n=239) and (2) Norwegian vancomycin-susceptible E. faecium (VSEfm) bacteraemia isolates from the national surveillance system for antimicrobial resistance in microbes (2008 and 2014; n=261) for further analysis. Whole-genome sequences were collected for population structure, van gene cluster, mobile genetic element and virulome analysis, as well as antimicrobial susceptibility testing. Comparative genomic and phylogeographical analyses were performed with complete genomes of global E. faecium strains from the National Center for Biotechnology Information (NCBI) (1946-2022; n=272). All Norwegian VREfm and most of the VSEfm clustered with global hospital-associated sequence types (STs) in the phylogenetic subclade A1. The vanB2 subtype carried by chromosomal Tn1549 integrative conjugative elements was the dominant van type. The major Norwegian VREfm cluster types (CTs) were in accordance with concurrent European CTs. The dominant vanB-type VREfm CTs, ST192-CT3/26 and ST117-CT24, were mostly linked to a single hospital in Norway where the clones spread after independent chromosomal acquisition of Tn1549. The less prevalent vanA VRE were associated with more diverse CTs and vanA carrying Inc18 or RepA_N plasmids with toxin-antitoxin systems. Only 5 % of the Norwegian VRE were Enterococcus faecalis, all of which contained vanB. The Norwegian VREfm and VSEfm isolates harboured CT-specific virulence factor (VF) profiles supporting biofilm formation and colonization. The dominant VREfm CTs in general hosted more virulence determinants than VSEfm. The phylogenetic clade B VSEfm isolates (n=21), recently classified as Enterococcus lactis, harboured fewer VFs than E. faecium in general, and particularly subclade A1 isolates. In conclusion, the population structure of Norwegian E. faecium isolates mirrors the globally prevalent clones and particularly concurrent European VREfm/VSEfm CTs. Novel chromosomal acquisition of vanB2 on Tn1549 from the gut microbiota, however, formed a single major hospital VREfm outbreak. Dominant VREfm CTs contained more VFs than VSEfm.

Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry.

Angular leaf spot disease caused by plant pathogenic bacterium Xanthomonas fragariae seriously threatens strawberry crop production globally. In this study, we sequenced the whole genome of X. fragariae YM2, isolated from Yunnan Province, China. In addition, we performed a comparative genome analysis of X. fragariae YM2 with two existing strains of X. fragariae YL19 and SHQP01 isolated from Liaoning and Shanghai, respectively. The results of Nanopore sequencing showed that X. fragariae YM2 comprises one single chromosome with a contig size of 4,263,697 bp, one plasmid contig size of 0.39 Mb, a GC content ratio of 62.27%, and 3,958 predicted coding genes. The genome of YM2 comprises gum, hrp, rpf, and xps gene clusters and lipopolysaccharide (LPS), which are typical virulence factors in Xanthomonas species. By performing a comparative genomic analysis between X. fragariae strains YM2, YL19, and SHQP01, we found that strain YM2 is similar to YL19 and SHQP01 regarding genome size and GC contents. However, there are minor differences in the composition of major virulence factors and homologous gene clusters. Furthermore, the results of collinearity analysis demonstrated that YM2 has lower similarity and longer evolutionary distance with YL19 and SHQP01, but YL19 is more closely related to SHQP01. The availability of this high-quality genetic resource will serve as a basic tool for investigating the biology, molecular pathogenesis, and virulence of X. fragariae YM2. In addition, unraveling the potential vulnerabilities in its genetic makeup will aid in developing more effective disease suppression control measures.